Chronic idiopathic inflammatory bowel disease (IBD) predisposes to the development of colorectal carcinoma. The molecular basis of this predisposition has been studied for many years, but much remains to be discovered. For example, we know that unique global gene expression patterns occur early in IBD-associated neoplasias (IBDNs), and that hypermethylation of certain promoter regions is a mechanism of gene inactivation in these lesions. But at which neoplastic stage do these alterations occur during IBD-associated carcinogenesis? Can individual genes be identified from global genomic screens of expression, methylation, or change in copy number? Which global patterns or individual gene alterations predict early neoplastic transformation or progression? The current proposal will answer these questions by developing the following unifying hypothesis: The hypothesis is that the study of IBDNs at all stages of evolution will benefit from global, comprehensive genomic approaches that will illuminate molecular genetic carcinogenetic pathways while simultaneously discovering clinically valuable neoplastic progression biomarkers. This hypothesis will be developed by pursuing the following Aims: 1. To perform a genome-wide characterization of the epigenetic signature of IBD-associated neoplasias (IBDNs), focusing on known as well as novel CpG islands in the promoter or upstream portions of genes. A. Known methylation targets will be analyzed, including E-cadherin (CDH 1), p 16, p 15, p 14-ARF, death-associated protein kinase (DAPK), O6-methylguanine DNA methyltransferase (MGMT), human mutL homolog 1 (hMLH 1), adenomatous polyposis coli (APC), RASSF1A, deleted in colon carcinoma (DCC), and 14-3-3-sigma. B. Searches for novel targets of methylation in IBDNs will be performed using CpG island microarrays. 2. To comprehensively scan the genome for alterations in gene copy number at each stage of IBD-neoplasia. A. To probe cDNA microarrays with genomic DNA in order to identify specific genes involved by DNA amplification and deletion in IBDNs. 3. To perform global gene expression studies of IBDNs using cDNA microarrays, a. To produce cDNA microarrays and probe them with RNAs from IBDNs at all stages of neoplasia, b. To use hierarchical clustering, significance analysis of microarrays (SAM) and artificial neural networks (ANNs) to identify global expression patterns and specific genes at each stage of IBD-associated neoplasia. 4. To perform clinical correlations with molecular data. A. Bioinformatics algorithms will be used to define gene expression patterns associated with neoplastic progression in IBDN. B. Clinical parameters will be correlated with gene expression, methylation and copy number data to delineate specific genes potentially relevant to neoplastic progression in IBD.